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Updated: May 4, 2026
09:14
Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
Published on: June 28, 2018
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A fast algorithm for genome-wide analysis of proteins with repeated sequences
M Pellegrini1, E M Marcotte, T O Yeates
1Molecular Biology Institute and UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, 90095-1570, USA.
Proteins
|June 26, 1999
Summary
A new algorithm efficiently finds repeating fragments in protein sequences. Eukaryotic proteins show more internal repeats, highlighting their role in protein evolution.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Protein sequences often contain internal repeating fragments.
- Identifying these repeats is crucial for understanding protein function and evolution.
- Existing methods may be computationally intensive.
Purpose of the Study:
- To develop a fast algorithm for detecting repeating fragments in protein sequences.
- To estimate the statistical significance of identified repeats.
- To analyze the prevalence of internal repeats across different organisms.
Main Methods:
- An extension of the Smith-Waterman algorithm was developed.
- The algorithm calculates sub-optimal alignments of a sequence against itself.
- Statistical significance of alignment scores and repeat characteristics (length, frequency) are determined.
Main Results:
- The algorithm efficiently identifies repeating fragments and their statistical significance.
- Eukaryotic proteins exhibit a higher frequency of internal repeats compared to prokaryotic and archaeal proteins.
- 18% of yeast and 28% of human protein sequences contain detectable repeats.
Conclusions:
- Internal duplication is a significant factor in protein evolution.
- The developed algorithm provides a rapid and effective tool for repeat detection.
- Comparative analysis reveals differences in repeat content across major domains of life.
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